Oncokb deletion

[jkobject]

Hi!

Thank you for the great tool! I am wondering why you have recently removed oncoKB. (This is a really useful annotator for us at DepMap)

Best,

[rkimoakbioinformatics]

@jkobject Sorry, it must have been a mistake. It has been restored.

[jkobject]

Hi!

I might not really understand how this repo work because oncoKB I don't see reverts on the master branch so oncokb seems to still be absent from this repo.

I tried to run the oncokb annotator a couple days ago and it seems to have returned null for every mutations (which seems unlikely).

[mryaninsilico]

Rick,

There may be a special case here but in general, I don’t think users who request support for OC should be pointed to your repo for fixes. I know you have been carrying the support load and that it looked like there would be no future support for OC but with the grant coming back on-line in the next few weeks, we should talk this over.

Mike

From: Rick Kim @.> Sent: Tuesday, April 12, 2022 9:50 AM To: KarchinLab/open-cravat-modules-karchinlab @.> Cc: Subscribed @.***> Subject: Re: [KarchinLab/open-cravat-modules-karchinlab] Oncokb deletion (Issue KarchinLab/open-cravat#220)

@jkobject https://github.com/jkobject I have reverted it but the deletion must have come back to the repo by another push.

I keep the updates I make on the oncokb module at https://github.com/rkimoakbioinformatics/oak-cravat-modules/tree/master/annotators/oncokb. Please see the readme there for how to use this module. Without token.txt file with an access API, the module's result will be empty. What you get with oc module install oncokb is the latest version in this repo.

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[jkobject]

Thanks for the help,

Should I ask my next question on the open Cravat's main repo?

I have ran the annotation with oncokb, listed the keyfile in the right folder, oncokb annotator ran for a long time and the output vcf was annotated but I see every mutations in the file having the exact same annotation: OC_oncokb__oncogenic=Unknown;OC_oncokb__knownEffect=Unknown

Moreover, it seems that oncokb is very slow (takes 2 days to annotate one WGS file)... We have thousands that we would want to annotate.

My guess is that it can only happen if you are making requests to the API for every mutations?

Would there be a way to make this process much faster?

1. keeping a record of oncoKB's annotations? or
2. only running it on coding regions? (it seems oncoKB only has annotation for these)

What do you think?

[drstormR]

Hi,
Did you find a solution for using OncoKB module with OpenCravat? I have the same issue, it's running extremely slow.

Thanks